Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Glassing, Angela; Dowd, Scot E.; Galandiuk, Susan; Davis, Brian; Chiodini, Rodrick J.

doi:10.1186/s13099-016-0103-7

Gut Pathogens

Table 2 Bacterial families and genera identified within the MoBio DNA extraction kit DNA from 81 bacterial genera and 108 tentative species were identified as inherent contaminants

From: Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Family	Genera	Relative %^a
Acetobacteraceae	Roseomonas	1.71
Actinomycetaceae	Actinomyces	0.03
Aerococcaceae	Abiotrophia	1.13
Alcanivoracaceae	Alcanivorax ^b	0.005
Alicyclobacillaceae	Tumebacillus	3.7
Alphaproteobacteria, unclassified	Candidatus_alysiosphaera ^b	0.003
Aurantimonadaceae	Aurantimonas ^b	0.002
Bacillaceae	Bacillus	0.3
Bacillales family xi. incertae sedis	Gemella ^b	0.005
Bacteroidaceae	Bacteroides	0.08
Bifidobacteriaceae	Bifidobacterium ^b	0.003
Bradyrhizobiaceae	Afipia ^b	0.001
Bradyrhizobiaceae	Bradyrhizobium	0.51
Burkholderiaceae	Burkholderia	0.12
Burkholderiaceae	Roseateles	1.31
Cardiobacteriaceae	Cardiobacterium	0.014
Carnobacteriaceae	Granulicatella	0.02
Carnobacteriaceae	Trichococcus ^b	0.002
Christensenellaceae	Christensenella ^b	0.002
Clostridiaceae	Clostridium	0.024
Clostridiales, unclassified	Flavonifractor ^b	0.002
Clostridiales, unclassified	Pseudoflavonifractor ^b	0.002
Clostridiales family xi. incertae sedis	Anaerococcus ^b	0.004
Comamonadaceae	Comamonas	0.037
	Coprococcus ^b	0.002
	Curvibacter	0.155
	Pseudorhodoferax	0.32
Coriobacteriaceae	Atopobium ^b	0.002
Coriobacteriaceae	Collinsella ^b	0.005
Corynebacteriaceae	Corynebacterium	2.2
Eggerthellaceae	Eggerthella ^b	0.007
Eggerthellaceae	Slackia ^b	0.002
Enterobacteriaceae	Escherichia	0.03
	Escherichia_Shigella ^b	0.003
	Klebsiella	0.02
	Serratia	0.007
Enterococcaceae	Enterococcus	0.008
Erysipelotrichaceae	Catenibacterium ^b	0.002
	Erysipelatoclostridium	0.02
	Solobacterium ^b	0.005
	Turicibacter	0.021
Eubacteriaceae	Eubacterium ^b	0.003
Flavobacteriaceae	Capnocytophaga	0.21
	Chryseobacterium	0.33
	Cloacibacterium	0.003
Fusobacteriaceae	Fusobacterium	0.28
Geodermatophilaceae	Blastococcus	0.25
Gordoniaceae	Gordonia	0.02
Halanaerobiaceae	Halocella ^b	0.005
Lachnospiraceae	Blautia	0.02
	Johnsonella ^b	0.002
	Lachnoanaerobaculum	0.23
	Lachnoclostridium ^b	0.005
	Lachnospira	0.007
	Moryella ^b	0.002
	Pseudobutyrivibrio	0.02
	Roseburia	0.009
	Tyzzerella ^b	0.002
Lactobacillaceae	Lactobacillus	0.009
Leptotrichiaceae	Leptotrichia	0.28
Methylobacteriaceae	Methylobacterium	11.7
Methylocystaceae	Methylopila ^b	0.003
Microbacteriaceae	Pseudoclavibacter ^b	0.005
Micrococcaceae	Arthrobacter	0.03
Micrococcaceae	Rothia ^b	0.002
Micromonosporaceae	Pilimelia ^b	0.002
Moraxellaceae	Enhydrobacter	1.95
Neisseriaceae	Kingella ^b	0.002
Neisseriaceae	Neisseria	0.05
Oxalobacteraceae	Janthinobacterium	0.002
	Massilia	0.11
	Oxalobacter	2.3
Paenibacillaceae	Brevibacillus	0.03
Paenibacillaceae	Paenibacillus ^b	0.003
Pasteurellaceae	Haemophilus	0.26
Pelagibacteraceae	Candidatus pelagibacter ^b	0.002
Peptococcaceae	Peptococcus ^b	0.003
Peptoniphilaceae	Parvimonas	0.02
Peptoniphilaceae	Peptoniphilus ^b	0.002
Peptostreptococcaceae	Intestinibacter	0.043
Phyllobacteriaceae	Phyllobacterium	0.3
Porphyromonadaceae	Porphyromonas ^b	0.003
Prevotellaceae	Prevotella	10.4
Prevotellaceae	Xylanibacter ^b	0.002
Propionibacteriaceae	Propionibacterium	15.8
Pseudomonadaceae	Pseudomonas	0.009
Rhodobacteraceae	Rubellimicrobium	0.78
Rikenellaceae	Alistipes	0.05
Ruminococcaceae	Anaerotruncus ^b	0.001
	Faecalibacterium	0.02
	Fastidiosipila ^b	0.003
	Oscillospira ^b	0.002
	Papillibacter ^b	0.003
	Ruminiclostridium ^b	0.003
	Ruminococcus	0.007
Sphingobacteriaceae	Sphingobacterium ^b	0.003
Staphylococcaceae	Staphylococcus	5.2
Streptococcaceae	Streptococcus	13.4
Sutterellaceae	Parasutterella ^b	0.005
Thermaceae	Meiothermus	0.06
tm7 (candidate division)	tm7 (candidate division)	0.44
Veillonellaceae	Dialister ^b	0.003
	Megasphaera	1.53
	Selenomonas	0.44
	Veillonella	20.4
Xanthomonadaceae	Stenotrophomonas	1.25

These taxa are unlikely to have been introduced by PCR kit reagents or contamination on the bench, and so are likely to have originated from the DNA extraction kit and during the DNA extraction process
See Additional file 1: Table S1 for list of tentative species identification
^aRelative percent prevalence are average of multiple lots
^bDetection of organism was lot dependent and not present in all lots

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ISSN: 1757-4749

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